Background Vaccination against Coronavirus provides adequate adaptive immunity to combat the infection; however, lack of knowledge and misinformation regarding COVID-19 vaccines leads to “Vaccine hesitancy” among people and halts the immunization process. Aim of this study is dispelling myths and misinformation via a pharmacist counseling and optimizing the vaccine acceptance to withstand this pandemic. Methods A prospective observational study was conducted in two phases at Quaid-i-Azam University (QAU), Islamabad and its peripheral rural area; 200 non-vaccinated individuals were recruited in the pre-intervention phase and 50 in the post-intervention phase. Interview based questionnaire filling was done in both the phases for highlighting the myths causing COVID-19 vaccine hesitancy, and major sources of spreading misinformation. Individuals were guided and counseled regarding misinformation about vaccination. Results In our study most of the respondents were females (70%). In current study, we counseled 50 participants from pre-intervention phase and significant difference has been seen in percentages. As in the pre-intervention phase, 77% individuals believed the myth that COVID-19 vaccine was developed too fast, and in the post-intervention phase it was reduced to 12% via counseling. Similarly 50% participants believed that vaccine is associated with COVID-19 illness that was decreased to 20% Highly prevailed myths included; too fast development of COVID vaccine (77%), its association with COVID-19 illness (72%), and doubt regarding its efficacy (53%). Chi square analysis found significant association between highly prevailed myths and education level. Study participants with higher education level were more reluctant as they were relying more on the misconceptions regarding COVID-19 vaccine (p-value > 0.05). Conclusion Awareness regarding misconception and myths via proper counseling played important role in eradicating vaccine hesitancy and optimizing its acceptance. Longer follow up studies on large sample size are required for convincing results.